Paternal genetic structure of an endogamous Saraiki population from Pakistan inferred from rapidly mutating Y-STRs

Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic genetics, but conventional panels show limited diversity and poor resolution among paternal relatives in endogamous populations. Rapidly mutating (RM) Y-STRs offer higher mutation rates to overcome these limitations.

To evaluate the forensic and population genetic utility of 13 RM Y-STRs in the endogamous Saraiki population of Pakistan.

Thirteen RM Y-STR loci were analysed in 100 unrelated Saraiki males. Haplotype diversity, discrimination capacity, allele frequencies, and gene diversity were calculated. Y-haplogroups were inferred, and demographic analyses (BATWING, mismatch distribution, median-joining networks) were performed. Population comparisons used Rst distances.

High haplotype diversity (0.9992) and discrimination capacity (0.9600) were observed, with 319 alleles across 13 loci. Allele frequencies ranged from 0.0050 to 0.3100, and gene diversity values were between 0.7700 and 0.9302. Twelve haplogroups were identified, with R1a (42%), R2 (18%), and J2 (15%) most frequent. Estimated coalescence times were ∼5,200 (R1a), ∼6,800 (R2), and ∼8,900 years (J2). Furthermore, mismatch distribution analyses suggested differing demographic histories. Network analyses confirmed the resolving power of multicopy RM Y-STRs for closely related lineages. Saraiki showed closest affinity to Punjabi and greatest divergence from Hazara populations.

RM Y-STRs provide substantially enhanced discriminatory power in the Saraiki population compared with conventional panels, with multicopy markers achieving discrimination comparable to the full 13-locus set. These data enrich global reference databases and support forensic and population genetic research in endogamous South Asian populations.